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Chemical Research in Chinese Universities 2024年第1期40卷 136-144页

作者： DU Xiaohui LI Encheng WANG Qi YOU Xin Lung Cancer Transitional Medicine Center The Second Affiliated Hospital of Dalian Medical UniversityDalian116023P.R.China Department of Scientific Research Center The Second Affiliated Hospital of Dalian Medical UniversityDalian116023P.R.China Department of Respiratory Medicine The Second Affiliated Hospital of Dalian Medical UniversityDalian116023P.R.China

Lung cancer produces a high incidence of malignant *** have been many studies on lung cancer using mass spectrometry(MS)***,most studies have focused on humoral *** this work,26 pairs of tissue samples(tumor ***-tumor)from patients with lung cancer were analyzed using liquid chromatography-tandem MS(LC-MS/MS)with data-independent acquisition *** total,3152 proteins were quantified from tissue samples with high confidence,including 189 up-regulated and 522 down-regulated proteins(tumor ***-tumor).In addition,79 and 690 proteins were identified only in para-cancerous samples and cancerous samples,*** results from bio-informatics tools indicated that altered proteins like PEBP1,HRG and LYZ could be ideal reservoirs for screening the potential biomarkers for lung *** is believed these tissue-specific proteomics results will assist in the studies of lung cancer.

关键词： Lung cancer proteome Data-independent aquisition

Comprehensive analyses of the proteome and ubiquitome revealed mechanism of high temperature accelerating petal abscission in tree peony

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Horticultural Plant Journal 2024年第1期10卷 205-222页

作者： Chunying Liu Ziqi Liu Yanchao Yuan Yuxi Zhang Yifu Fang Junqiang Chen Shupeng Gai Key Laboratory of Plant Biotechnology in Shandong Province College of Life SciencesQingdao Agricultural UniversityQingdaoShandong 266109China Shandong Academy of Forestry JinanShandong 250014China

Tree peony(Paeonia suffruticosa Andrews)is a well-known ornamental plant with high economic value,but the short fluorescence is a key obstacle to its ornamental value and industry *** temperature accelerates flower senescence and abscission,but the associated mechanisms are poorly *** this study,the tandem mass tag(TMT)proteome and label-free quantitative ubiquitome from tree peony cut flowers treated with 20℃for 0 h(RT0),20℃or 28℃for 60 h(RT60 or HT60)were examined based on morphological observation,***,6970 proteins and 1545 lysine ubiquitinated(Kub)sites in 844 proteins were *** residues(such as glutamate and aspartate)neighboring the Kub sites were in preference,and 36.01%of the Kub sites were located on the protein *** differentially expressed proteins(DEPs)and Kub-DEPs in HT60 vs RT60 were mainly enriched in ribosomal protein,protein biosynthesis,secondary metabolites biosynthesis,flavonoid metabolism,carbohydrate catabolism,and auxin biosynthesis and signaling revealed by GO and KEGG analysis,accompanying the increase of endogenous abscisic acid(ABA)accumulation and decrease of endogenous indoleacetic acid(IAA)***,the expression patterns of six enzymes(SAMS,ACO,YUC,CHS,ANS and PFK)putatively with Kub modifications were analyzed by proteome and real-time quantitative *** cell-free degradation assays showed PsSAMS and PsACO proteins could be degraded via the 26 S proteasome system in tree peony ***,a working model was proposed for the acceleration of flower senescence and abscission by high *** summary,all results contributed to understanding the mechanism of flower senescence induced by high temperature and prolonging fluorescence in tree peony.

关键词： Tree peony proteome Ubiquitome High temperature Flower senescence

Differences in vascular endothelial function and serum proteome between obese people with phlegm-dampness constitution and balanced constitution

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Journal of Traditional Chinese Medicine 2024年第1期44卷 188-196页

作者： ZHU Linghui SUN Ziwei GUAN Yuanyuan LIU Meiyi ZHENG Yi YU Ruoxi WANG Qi LI Lingru School of Chinese Medicine Beijing University of Chinese MedicineBeijing 102488China National Institute of TCM Constitution and Preventive Medicine Beijing University of Chinese MedicineBeijing 100029China

OBJECTIVE:To evaluate the extent of vascular endothelial dysfunction and preliminary identify serum protein biomarkers associated with obese individuals at risk for cardiovascular disease(CVD).METHODS:Fifteen obese volunteers with the phlegmdampness constitution or balanced constitution were recruited for this study *** clinical baseline data was collected,and the vascular endothelial function was evaluated using the EndoPAT?.Blood samples were collected for the serum proteome *** differences in the serum protein expression levels between the two groups were detected and the protein interaction network analysis,correlation analysis,receiver operating characteristic(ROC)curve analysis,and random forest model investigation were ***:There were no statistical differences found in the baseline *** vascular endothelial function,the reactive hyperemia index(RHI)of the phlegm-dampness constitution obese group was significantly lower than that of the balanced constitution obese group(1.46±0.30 vs 2.82±0.78,P<0.0001),indicating vascular endothelial *** are 66 differentially expressed serum proteins between the two *** A2(Apo A2),angiotensin-converting enzyme 2(ACE-2),interleukin-33(IL-33),and forkhead box P3(FoxP3)showed significant differences and area under curve values of their ROC curves were greater than 0.7 and correlated significantly with ***:Vascular endothelial dysfunction was present in the phlegm-dampness constitution obese ***,alterations in the expression levels of key serum proteins,including Apo A2,ACE-2,IL-33,and Fox P3 could serve as potential biomarkers in the obese population at risk of CVD.

关键词： obesity phlegm-dampness constitution vascular endothelial function proteome reactive hyperemia index

In‑depth proteome characterization of endometrium and extraembryonic membranes during implantation in pig

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Journal of Animal Science and Biotechnology 2024年第3期15卷 1027-1055页

作者： Maria A.Gil Josep M.Cambra Heriberto Rodriguez‑Martinez Cristina Cuello Inmaculada Parrilla Emilio A.Martinez Department of Medicine and Animal Surgery International Excellence Campus for Higher Education and Research“Campus Mare Nostrum”University of MurciaMurciaSpain Institute for Biomedical Research of Murcia(IMIB-Pascual Parrilla) MurciaSpain Technical University of Munich MunichGermany Department of Biomedical&Clinical Sciences(BKV) BKH/Obstetrics&GynaecologyLinkoping UniversityLinkopingSweden

Background proteome characterization of the porcine endometrium and extraembryonic membranes is important to understand mother-embryo *** this study,the proteome of the endometrium and cho-rioallantoic membrane was characterized in pregnant sows(PS)during early gestation(d 18 and 24 of gestation)and in the endometrium of non-pregnant sows(NPS)during the same days using LC-MS/MS *** UniProtKB database and ClueGO were used to obtain functional Gene Ontology annotations and biological and functional networks,*** Our analysis yielded 3,254 and 3,457 proteins identified in the endometrium of PS and NPS,respectively;of these,1,753 being common while 1,501 and 1,704 were exclusive to PS and NPS,*** addition,we iden-tified 3,968 proteins in the extraembryonic membranes of *** analyses of function revealed some proteins had relevance for the immune system process and biological adhesion in endometrium while the embryonic chorion displayed abundance of proteins related to cell adhesion and cytoskeletal organization,suggesting they dominated the moment of endometrial remodeling,implantation and adhesion of the lining *** are available via Pro-teomeXchange with identifier *** This is the first in-depth proteomic characterization of the endometrium and extraembryonic mem-branes during weeks 3 to 4 of gestation;data that contribute to the molecular understanding of the dynamic environ-ment during this critical period,associated with the majority of pregnancy losses.

关键词： Endometrium Extraembryonic membranes Implantation Pig proteome

proteome and genome integration analysis of obesity

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Chinese Medical Journal 2023年第8期136卷 910-921页

作者： Qigang Zhao Baixue Han Qian Xu Tao Wang Chen Fang Rui Li Lei Zhang Yufang Pei Department of Epidemiology and Biostatistics School of Public HealthSuzhou Medical College of Soochow UniversitySuzhouJiangsu 215123China Jiangsu Key Laboratory of Preventive and Translational Medicine for Geriatric Diseases Suzhou Medical College of Soochow UniversitySuzhouJiangsu 215213China Department of Endocrinology The Second Affiliated HospitalSoochow UniversitySuzhouJiangsu 215004China Department of Gastroenterology The First Affiliated HospitalSoochow UniversitySuzhouJiangsu 215006China Center for Genetic Epidemiology and Genomics School of Public HealthSuzhou Medical College of Soochow UniversitySuzhouJiangsu 215123China

The prevalence of obesity has increased worldwide in recent *** factors are now known to play a substantial role in the predisposition to obesity and may contribute up to 70%of the risk for *** advancements during the last decades have allowed the identification of many hundreds of genetic markers associated with ***,the transformation of current genetic variant-obesity associations into biological knowledge has been proven *** and proteomics are complementary fields,as proteomics extends functional *** genomic and proteomic data can help to bridge a gap in knowledge regarding genetic variant-obesity associations and to identify new drug targets for the treatment of *** provide an overview of the published papers on the integrated analysis of proteomic and genomic data in obesity and summarize four mainstream strategies:overlap,colocalization,Mendelian randomization,and proteome-wide association *** integrated analyses identified many obesity-associated proteins,such as leptin,follistatin,and adenylate cyclase *** great progress,integrative studies focusing on obesity are still *** is an increased demand for large prospective cohort studies to identify and validate findings,and further apply these findings to the prevention,intervention,and treatment of *** addition,we also discuss several other potential integration methods.

关键词： Obesity Integration analysis Genome-wide association study proteome

Identification of transition factors in myotube formation from proteome and transcriptome analyses

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Journal of Integrative Agriculture 2023年第10期22卷 3135-3147页

作者： ZHENG Qi HU Rong-cui ZHU Cui-yun JING Jing LOU Meng-yu ZHANG Si-huan LI Shuang CAO Hong-guo ZHANG Xiao-rong LING Ying-hui College of Animal Science and Technology Anhui Agricultural UniversityHefei 230036P.R.China Key Laboratory of Embryo Development and Reproductive Regulation of Anhui Province Fuyang Normal UniversityFuyang 236041P.R.China Anhui Province Key Laboratory of Local Livestock and Poultry Genetic Resource Conservation and Bio-Breeding Anhui Agricultural UniversityHefei 230036P.R.China

Muscle fibers are the main component of skeletal muscle and undergo maturation through the formation of *** early development,a population of skeletal muscle satellite cells(SSCs)proliferate into *** myoblasts then undergo further differentiation and fusion events,leading to the development of ***,the mechanisms involved in the transition from SSCs to myotube formation remain *** this study,we characterized changes in the proteomic and transcriptomic expression profiles of SSCs,myoblasts(differentiation for 2 d)and myotubes(differentiation for 10 d).Proteomic analysis identified SLMAP and STOM as potentially associated with myotube *** addition,some different changes in MyoD,MyoG,Myosin7 and Desmin occurred after silencing SLMAP and STOM,suggesting that they may affect changes in the myogenic *** analysis indicated that the differentiation and migration factors SVIL,ENSCHIG00000026624(AQP1)and SERPINE1 enhanced the transition from SSCs to myoblasts,accompanied by changes in the apoptotic *** the myoblast *** group,candidates related to cell adhesion and signal transduction were highly expressed in the ***,CCN2,TGFB1,MYL2 and MYL4 were identified as hub-candidates in this *** data enhance our existing understanding of myotube formation during early development and repair.

关键词： proteome transcriptome skeletal muscle satellite cells myoblast myotube

The proteome Landscape of Human Placentas for Monochorionic Twins with Selective Intrauterine Growth Restriction

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Genomics, Proteomics & Bioinformatics 2023年第6期21卷 1246-1259页

作者： Xin-Lu Meng Peng-Bo Yuan Xue-Ju Wang Jing Hang Xiao-Ming Shi Yang-Yu Zhao Yuan Wei Department of Obstetrics and Gynecology Peking University Third HospitalBeijing 100191China Center for Reproductive Medicine Department of Obstetrics and GynecologyPeking University Third HospitalBeijing 100191China Key Laboratory of Assisted Reproduction Ministry of EducationBeijing 100191China Beijing Key Laboratory of Reproductive Endocrinology and Assisted Reproduction Beijing 100191China National Clinical Research Center for Obstetrics and Gynecology Beijing 100191China

In perinatal medicine,intrauterine growth restriction(IUGR)is one of the greatest *** etiology of IUGR is multifactorial,but most cases are thought to arise from placental ***,identifying the placental cause of IUGR can be difficult due to numerous confounding *** IUGR(sIUGR)would be a good model to investigate how impaired placentation affects fetal development,as the growth discordance between monochorionic twins cannot be explained by confounding genetic or maternal ***,we constructed and analyzed the placental proteomic profiles of IUGR twins and normal ***,we identified a total of 5481 proteins,of which 233 were differentially expressed(57 up-regulated and 176 down-regulated)in IUGR *** analysis indicates that these differentially expressed proteins(DEPs)are mainly associated with cardiovascular system development and function,organismal survival,and organismal ***,34 DEPs are significantly enriched in angiogenesis,and diminished placental angiogenesis in IUGR twins has been further elaborately ***,we found decreased expression of metadherin(MTDH)in the placentas of IUGR twins and demonstrated that MTDH contributes to placental angiogenesis and fetal growth in ***,our findings reveal the comprehensive proteomic signatures of placentas for sIUGR twins,and the DEPs identified may provide in-depth insights into the pathogenesis of placental dysfunction and subsequent impaired fetal growth.

关键词： Selective intrauterine growth restriction Placenta proteome Angiogenesis Metadherin

The proteome of distal nerves: implication in delayed repair and poor functional recovery

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Neural Regeneration Research 2022年第9期17卷 1998-2006页

作者： Song Guo Raymond M.Moore M.Cristine Charlesworth Kenneth L.Johnson Robert J.Spinner Anthony J.Windebank Huan Wang Department of Neurologic Surgery Mayo ClinicRochesterMNUSA Biomedical Statistics and Informatics Mayo ClinicRochesterMNUSA Proteomics Core Mayo ClinicRochesterMNUSA Department of Neurology Mayo ClinicRochesterMNUSA

Chronic denervation is one of the key factors that affect nerve *** axotomy deteriorates the distal nerve stump,causes protein changes,and renders the microenvironment less permissive for *** of these factors/proteins have been individually *** better delineate the comprehensive protein expression profiles and identify proteins that contribute to or are associated with this detrimental effect,we carried out a proteomic analysis of the distal nerve using an established delayed rat sciatic nerve repair *** rats that received immediate repair after sciatic nerve transection served as control,whereas four rats in the experimental group(chronic denervation)had their sciatic nerve repaired after a 12-week *** the rats were sacrificed after 16 weeks to harvest the distal nerves for extracting ***-five micrograms of protein from each sample were fractionated in SDS-PAGE ***-MS/MS analysis was applied to the *** expression levels of nerves on the surgery side were compared to those on the contralateral *** protein with a P value of less than 0.05 and a fold change of 4 or higher was deemed differentially *** the differentially expressed proteins in both groups were further stratified according to the biological processes.A PubMed search was also conducted to identify the differentially expressed proteins that have been reported to be either beneficial or detrimental to nerve *** Pathway Analysis(IPA)software was used for pathway *** results showed that 709 differentially expressed proteins were identified in the delayed repair group,with a bigger proportion of immune and inflammatory process-related proteins and a smaller proportion of proteins related to axon regeneration and lipid metabolism in comparison to the control group where 478 differentially expressed proteins were *** experimental group also had more beneficial proteins that were d

关键词： chronic axotomy chronic denervation delayed repair distal nerve functional recovery nerve regeneration peripheral nerve prolonged denervation proteome sciatic nerve sciatic nerve transection

Improving the genome and proteome annotations of the marine model diatom Thalassiosira pseudonana using a proteogenomics strategy

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Marine Life Science & Technology 2023年第1期5卷 102-115页

作者： Xiao-Huang Chen Ming-Kun Yang Yuan-Yuan Li Zhang-Xian Xie Shu-Feng Zhang Mats Töpel Shady A.Amin Lin Lin Feng Ge Da-Zhi Wang State Key Laboratory of Marine Environmental Science/College of the Environment and Ecology Xiamen UniversityXiamen361005China Southern Marine Science and Engineering Guangdong Laboratory(Zhuhai) Sun Yat-Sen UniversityZhuhai519082China Key Laboratory of Algal Biology Institute of HydrobiologyChinese Academy of SciencesWuhan430072China College of Chemistry Chemical Engineering and EnvironmentMinnan Normal UniversityZhangzhou363000China Department of Marine Sciences University of GothenburgBox 46140530GothenburgSweden IVL-Swedish Environmental Research Institute Box 5302140014GothenburgSweden New York University Abu Dhabi Saadiyat Island129188Abu DhabiUnited Arab Emirates

Diatoms are unicellular eukaryotic phytoplankton that account for approximately 20%of global carbon fixation and 40%of marine primary productivity;thus,they are essential for global carbon biogeochemical cycling and *** availability of ten diatom genome sequences has facilitated evolutionary,biological and ecological research over the past decade;however,a complimentary map of the diatom proteome with direct measurements of proteins and peptides is still ***,we present a proteome map of the model marine diatom Thalassiosira pseudonana using high-resolution mass spectrometry combined with a proteogenomic ***-depth proteomic profiling of three different growth phases and three nutrient-deficient samples identified 9526 proteins,accounting for~81%of the predicted protein-coding *** analysis identified 1235 novel genes,975 revised genes,104 splice variants and 234 single amino acid ***,our quantitative proteomic analysis experimentally demonstrated that a considerable number of novel genes were differentially translated under different nutrient *** findings substantially improve the genome annotation of *** and provide insights into new biological functions of *** relatively comprehensive diatom proteome catalog will complement available diatom genome and transcriptome data to advance biological and ecological research of marine diatoms.

关键词： Marine diatoms Thalassiosira pseudonana proteome Proteogenomics

The ionome and proteome landscape of aging in laying hens and relation to egg white quality

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中国科学:生命科学英文版 2023年第9期66卷 2020-2040页

作者： Guang Li Yuqing Feng Jian Cui Qihang Hou Tanfang Li Meiting Jia Zhengtian lv Qiuyu Jiang Ying Wang Ming Zhang Lin Wang Zengpeng Lv Junyou Li Yuming Guo Bingkun Zhang State Key Laboratory of Animal Nutrition and Feeding China Agricultural UniversityBeijing 100193China Sichuan Tieqilishi Industrial Co. Ltd.Mianyang 621010China Sichuan Sundaily Farm Ecological Food Co. Ltd.Mianyang 621010China Graduate School of Agricultural and Life Sciences The University of TokyoIbaraki 319-0206Japan

The ionome is essential for maintaining body function and health status by participating in diverse key biological ***, the distribution and utilization of ionome among different organs and how aging impacts the ionome leading to a decline in egg white quality remain unknown. Thus, we used inductively coupled plasma mass spectrometry(ICP-MS) to analyze 35 elements and their isotopic contents in eight organs of laying hens at 35, 72, and 100 weeks. Moreover, the magnum proteome, amino acids in egg white, and egg white quality were analyzed in laying hens at three different ages using 4D proteomics techniques, an amino acid analyzer, and an egg quality analyzer. Across the organs, we identified varying distribution patterns among macroelements(Mg24, Ca43/44, K39, and P31), transition metals(Zn64/66, Cu63/65, Fe56/57, and Mn55), and toxic elements(Pb208, Ba137, and Sr86). We observed an organ-specific aging pattern characterized by the accumulation of toxic elements(Pb208, Ba137, and Sr86) and calcification in the small intestine. Additionally, a decrease in the utilization of essential trace elements selenium(Se78/82) and manganese(Mn55) was noted in the oviduct. By analyzing ionome in tandem with egg quality, egg white amino acids, and proteome, we unveiled that the reduction of selenium and manganese concentrations in the magnum during the aging process affected amino acid metabolism, particularly tryptophan metabolism, thereby inhibiting the amino acid synthesis in the magnum. Furthermore, it accelerated the senescence of magnum cells through necroptosis activation, leading to a decline in the albumen secretion function of the magnum and subsequently reducing egg white ***, this study provides insights into the evolution of 35 elements and their isotopes across 8 organs of laying hens with *** also reveals the elemental composition, interactions, and utilization patterns of these organs, as well as their correlation with egg white

关键词： aging elements ionome isotopes laying hens proteome